[English] 日本語
Yorodumi
- PDB-4mqa: Human beta-tryptase co-crystal structure with {(1,1,3,3-tetrameth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mqa
TitleHuman beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)
ComponentsTryptase alpha/beta-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / coferon / alpha-hydroxyketone / small molecule inhibitor / drug discovery / self-assembly / crystal catalysis / silanol / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / defense response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-X00 / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWhite, A. / Lakshminarasimhan, D. / Suto, R.
CitationJournal: To be Published
Title: Target-directed self-assembly of homodimeric drugs
Authors: Giardina, S.F. / Pingle, M. / Foreman, K.W. / Werner, D.S. / Bergstrom, D.E. / Barany, F. / Arnold, L.D.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptase alpha/beta-1
B: Tryptase alpha/beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4699
Polymers54,9832
Non-polymers1,4867
Water4,197233
1
A: Tryptase alpha/beta-1
B: Tryptase alpha/beta-1
hetero molecules

A: Tryptase alpha/beta-1
B: Tryptase alpha/beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,93718
Polymers109,9664
Non-polymers2,97214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area10230 Å2
ΔGint-190 kcal/mol
Surface area38470 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-86 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.168, 78.168, 165.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Tryptase alpha/beta-1 / Tryptase-1 / Tryptase I / Tryptase alpha-1


Mass: 27491.426 Da / Num. of mol.: 2 / Fragment: UNP residues 31-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPS1, TPS2, TPSAB1, TPSB1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q15661, tryptase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-X00 / {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)


Mass: 811.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H58N4O3S2Si2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN132K IS A NATURAL VARIANT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.9 mg/mL protein incubated with compound 13A 30 minutes on ice prior to setup with 30% PEG3350, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 28420 / Num. obs: 28363 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.123 / Χ2: 1.221 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.3310.60.4727720.8841100
2.33-2.4210.70.39280911100
2.42-2.5310.70.32628001.1061100
2.53-2.6710.80.26127871.2191100
2.67-2.8310.80.21428011.3361100
2.83-3.0510.70.16928141.4481100
3.05-3.3610.50.12928471.531100
3.36-3.85100.10528401.384199.7
3.85-4.859.30.08528751.143199
4.85-509.80.07330181.152199.2

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→35.36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.259 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.261 / ESU R Free: 0.227 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 1431 5.1 %RANDOM
Rwork0.1771 ---
all0.1808 28420 --
obs0.1808 28314 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.69 Å2 / Biso mean: 34.8129 Å2 / Biso min: 15.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.28 Å2-0 Å2
2--0.28 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 93 233 4162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194085
X-RAY DIFFRACTIONr_bond_other_d0.0010.023777
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9585608
X-RAY DIFFRACTIONr_angle_other_deg0.8623.0068673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7245488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54823.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52215591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4531525
X-RAY DIFFRACTIONr_chiral_restr0.1080.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02957
LS refinement shellResolution: 2.25→2.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 109 -
Rwork0.176 1920 -
all-2029 -
obs--99.22 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more